The chiral feature is a critical factor for the efficacy and safety of many therapeutic agents. At present, about 57% of marketed drugs are chiral drugs and about 99% of purified natural products are chiral compounds. There has been a tremendous potential of functional microorganisms and biocatalysts derived from them for the bioconversion of synthetic chemicals into drugs with high enantio-, chemo-, and regio-selectivities. Biocatalysis is becoming a key subassembly in the medicinal chemist's toolbox. In fact, the intermediates of many important therapeutic agents such as sitagliptin, pregabalin, ragaglitazar, paclitaxel, epothilone, abacavir, atorvastatin, rosuvastatin, and omapatrilat have been successfully synthesized via biocatalysis. In this review, various biocatalytic systems that enable to synthesize these chiral drug intermediates are updated and discussed regarding their potential application in the pharmaceutical industry. Further development and increased utilization of biocatalysis for production of drugs with emphasis on green chemistry can be expected.